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- Volume 56, 2002
Annual Review of Microbiology - Volume 56, 2002
Volume 56, 2002
- Preface
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- Review Articles
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Chances and Choices: Cold Spring Harbor 1944–1955
Vol. 56 (2002), pp. 1–15More LessThe author describes the circumstances and events that led her to begin graduate work in genetics at Columbia University in 1941 and to spend the summer of 1944 and the years 1945–1955 at the Department of Genetics of the Carnegie Institution of Washington at Cold Spring Harbor. She then recalls incidents and recounts anecdotes meant to convey something of the atmosphere of that place during those memorable years.
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Function of Pseudomonas Porins in Uptake and Efflux
Vol. 56 (2002), pp. 17–38More Less▪ AbstractPorins are proteins that form water-filled channels across the outer membranes of Gram-negative bacteria and thus make this membrane semipermeable. There are four types of porins: general/nonspecific porins, substrate-specific porins, gated porins, and efflux porins (also called channel-tunnels). The recent publication of the genomic sequence of Pseudomonas aeruginosa PAO1 has dramatically increased our understanding of the porins of this organism. In particular this organism has 3 large families of porins: the OprD family of specific porins (19 members), the OprM family of efflux porins (18 members), and the TonB-interacting family of gated porins (35 members). These familial relationships underlie functional similarities such that well-studied members of these families become prototypes for other members. We summarize here the latest information on these porins.
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The Bittersweet Interface of Parasite and Host: Lectin-Carbohydrate Interactions During Human Invasion by the Parasite Entamoeba histolytica
Vol. 56 (2002), pp. 39–64More Less▪ AbstractEntamoeba histolytica, as its name suggests, is an enteric parasite with a remarkable ability to lyse host tissues. However, the interaction of the parasite with the host is more complex than solely destruction and invasion. It is at the host-parasite interface that cell-signaling events commit the parasite to (a) commensal, noninvasive infection, (b) developmental change from trophozoite to cyst, or (c) invasion and potential death of the human host. The molecule central to these processes is an amebic cell surface protein that recognizes the sugars galactose (Gal) and N-acetylgalactosamine (GalNAc) on the surface of host cells. Engagement of the Gal/GalNAc lectin to the host results in cytoskeletal reorganization in the parasite. The parasite cytoskeleton regulates the extracellular adhesive activity of the lectin and recruits to the host-parasite interface factors required for parasite survival within its host. If the parasite lectin attaches to the host mucin glycoproteins lining the intestine, the result is commensal infection. In contrast, attachment of the lectin to a host cell surface glycoprotein leads to lectin-induced host cell calcium transients, caspase activation, and destruction via apoptosis. Finally, trophozoite quorum sensing via the lectin initiates the developmental pathway resulting in encystment. The structure and function of the lectin that controls these divergent cell biologic processes are the subject of this review.
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Heavy Metal Mining Using Microbes1
Vol. 56 (2002), pp. 65–91More Less▪ AbstractThe use of acidiphilic, chemolithotrophic iron- and sulfur-oxidizing microbes in processes to recover metals from certain types of copper, uranium, and gold-bearing minerals or mineral concentrates is now well established. During these processes insoluble metal sulfides are oxidized to soluble metal sulfates. Mineral decomposition is believed to be mostly due to chemical attack by ferric iron, with the main role of the microorganisms being to reoxidize the resultant ferrous iron back to ferric iron. Currently operating industrial biomining processes have used bacteria that grow optimally from ambient to 50°C, but thermophilic microbes have been isolated that have the potential to enable mineral biooxidation to be carried out at temperatures of 80°C or higher. The development of higher-temperature processes will extend the variety of minerals that can be commercially processed.
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Microsporidia: Biology and Evolution of Highly Reduced Intracellular Parasites
Vol. 56 (2002), pp. 93–116More Less▪ AbstractMicrosporidia are a large group of microbial eukaryotes composed exclusively of obligate intracellular parasites of other eukaryotes. Almost 150 years of microsporidian research has led to a basic understanding of many aspects of microsporidian biology, especially their unique and highly specialized mode of infection, where the parasite enters its host through a projectile tube that is expelled at high velocity. Molecular biology and genomic studies on microsporidia have also drawn attention to many other unusual features, including a unique core carbon metabolism and genomes in the size range of bacteria. These seemingly simple parasites were once thought to be the most primitive eukaryotes; however, we now know from molecular phylogeny that they are highly specialized fungi. The fungal nature of microsporidia indicates that microsporidia have undergone severe selective reduction permeating every level of their biology: From cell structures to metabolism, and from genomics to gene structure, microsporidia are reduced.
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Bacteriocins: Evolution, Ecology, and Application
Vol. 56 (2002), pp. 117–137More Less▪ AbstractMicrobes produce an extraordinary array of microbial defense systems. These include classical antibiotics, metabolic by-products, lytic agents, numerous types of protein exotoxins, and bacteriocins. The abundance and diversity of this potent arsenal of weapons are clear. Less clear are their evolutionary origins and the role they play in mediating microbial interactions. The goal of this review is to explore what we know about the evolution and ecology of the most abundant and diverse family of microbial defense systems: the bacteriocins. We summarize current knowledge of how such extraordinary protein diversity arose and is maintained in microbial populations and what role these toxins play in mediating microbial population-level and community-level dynamics. In the latter half of this review we focus on the potential role bacteriocins may play in addressing human health concerns and the current role they serve in food preservation.
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Evolution of Drug Resistance in Candida Albicans
Vol. 56 (2002), pp. 139–165More Less▪ AbstractThe widespread deployment of antimicrobial agents in medicine and agriculture is nearly always followed by the evolution of resistance to these agents in the pathogen. With the limited availability of antifungal drugs and the increasing incidence of opportunistic fungal infections, the emergence of drug resistance in fungal pathogens poses a serious public health concern. Antifungal drug resistance has been studied most extensively with the yeast Candida albicans owing to its importance as an opportunistic pathogen and its experimental tractability relative to other medically important fungal pathogens. The emergence of antifungal drug resistance is an evolutionary process that proceeds on temporal, spatial, and genomic scales. This process can be observed through epidemiological studies of patients and through population-genetic studies of pathogen populations. Population-genetic studies rely on sampling of the pathogen in patient populations, serial isolations of the pathogen from individual patients, or experimental evolution of the pathogen in nutrient media or in animal models. Predicting the evolution of drug resistance is fundamental to prolonging the efficacy of existing drugs and to strategically developing and deploying novel drugs.
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Bioterrorism: From Threat to Reality
Vol. 56 (2002), pp. 167–185More Less▪ AbstractThe fears and predictions of attacks with biological weapons, which were increasing at the close of the twentieth century, were transformed into reality not long after September 11, 2001, when several anthrax-laden letters were sent through the U.S. postal system. The attack challenged our medical preparedness and scientific understanding of the epidemiology of biothreat agents. It is fortunate that this was not a massive aerosol release that could have exposed hundreds of thousands. Rapid diagnoses and medical treatments limited casualties and increased survival rates, but tragically some individuals died of inhalational anthrax. Even as physicians tested new treatment regimes and scientists employed new ways of detecting anthrax and decontaminating the mail, new predictions were made for potentially even more devastating attacks with anthrax, smallpox, plague, tularemia, botulism, or hemorrhagic fever viruses. Fear gripped the nation. Law enforcement sought to find the villain(s) who sent the anthrax letters and to deter future bioterrorist attacks. The biomedical community began to seek new ways of protecting against such future threats of bioterrorism.
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Biofilms as Complex Differentiated Communities
Vol. 56 (2002), pp. 187–209More Less▪ AbstractProkaryotic biofilms that predominate in a diverse range of ecosystems are often composed of highly structured multispecies communities. Within these communities metabolic activities are integrated, and developmental sequences, not unlike those of multicellular organisms, can be detected. These structural adaptations and interrelationships are made possible by the expression of sets of genes that result in phenotypes that differ profoundly from those of planktonically grown cells of the same species. Molecular and microscopic evidence suggest the existence of a succession of de facto biofilm phenotypes. We submit that complex cell-cell interactions within prokaryotic communities are an ancient characteristic, the development of which was facilitated by the localization of cells at surfaces. In addition to spatial localization, surfaces may have provided the protective niche in which attached cells could create a localized homeostatic environment. In a holistic sense both biofilm and planktonic phenotypes may be viewed as integrated components of prokaryote life.
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Microbial Communities and Their Interactions in Soil and Rhizosphere Ecosystems
Vol. 56 (2002), pp. 211–236More Less▪ AbstractSince the first estimate of prokaryotic abundance in soil was published, researchers have attempted to assess the abundance and distribution of species and relate this information on community structure to ecosystem function. Culture-based methods were found to be inadequate to the task, and as a consequence a number of culture-independent approaches have been applied to the study of microbial diversity in soil. Applications of various culture-independent methods to descriptions of soil and rhizosphere microbial communities are reviewed. Culture-independent analyses have been used to catalog the species present in various environmental samples and also to assess the impact of human activity and interactions with plants or other microbes on natural microbial communities. Recent work has investigated the linkage of specific organisms to ecosystem function. Prospects for increased understanding of the ecological significance of particular populations through the use of genomics and microarrays are discussed.
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Transition Metal Transport in Yeast
Vol. 56 (2002), pp. 237–261More Less▪ AbstractAll eukaryotes and most prokaryotes require transition metals. In recent years there has been an enormous advance in our understanding of how these metals are transported across the plasma membrane. Much of this understanding has resulted from studies on the budding yeast Saccharomyces cerevisiae. A variety of genetic and biochemical approaches have led to a detailed understanding of how transition metals such as iron, copper, manganese, and zinc are acquired by cells. The regulation of metal transport has been defined at both the transcriptional and posttranslational levels. Results from studies on S. cerevisiae have been used to understand metal transport in other species of yeast as well as in higher eukaryotes.
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Inteins: Structure, Function, and Evolution
Vol. 56 (2002), pp. 263–287More Less▪ AbstractInteins are genetic elements that disrupt the coding sequence of genes. However, in contrast to introns, inteins are transcribed and translated together with their host protein. Inteins appear most frequently in Archaea, but they are found in organisms belonging to all three domains of life and in viral and phage proteins. Most inteins consist of two domains: One is involved in autocatalytic splicing, and the other is an endonuclease that is important in the spread of inteins. This review focuses on the evolution and technical application of inteins and only briefly summarizes recent advances in the study of the catalytic activities and structures of inteins. In particular, this review considers inteins as selfish or parasitic genetic elements, a point of view that explains many otherwise puzzling aspects of inteins.
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Type IV Pili and Twitching Motility
Vol. 56 (2002), pp. 289–314More Less▪ AbstractTwitching motility is a flagella-independent form of bacterial translocation over moist surfaces. It occurs by the extension, tethering, and then retraction of polar type IV pili, which operate in a manner similar to a grappling hook. Twitching motility is equivalent to social gliding motility in Myxococcus xanthus and is important in host colonization by a wide range of plant and animal pathogens, as well as in the formation of biofilms and fruiting bodies. The biogenesis and function of type IV pili is controlled by a large number of genes, almost 40 of which have been identified in Pseudomonas aeruginosa. A number of genes required for pili assembly are homologous to genes involved in type II protein secretion and competence for DNA uptake, suggesting that these systems share a common architecture. Twitching motility is also controlled by a range of signal transduction systems, including two-component sensor-regulators and a complex chemosensory system.
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The Class Mesomycetozoea: A Heterogeneous Group of Microorganisms at the Animal-Fungal Boundary*
Vol. 56 (2002), pp. 315–344More Less▪ AbstractWhen the enigmatic fish pathogen, the rosette agent, was first found to be closely related to the choanoflagellates, no one anticipated finding a new group of organisms. Subsequently, a new group of microorganisms at the boundary between animals and fungi was reported. Several microbes with similar phylogenetic backgrounds were soon added to the group. Interestingly, these microbes had been considered to be fungi or protists. This novel phylogenetic group has been referred to as the DRIP clade (an acronym of the original members: Dermocystidium, rosette agent, Ichthyophonus, and Psorospermium), as the class Ichthyosporea, and more recently as the class Mesomycetozoea. Two orders have been described in the mesomycetozoeans: the Dermocystida and the Ichthyophonida. So far, all members in the order Dermocystida have been pathogens either of fish (Dermocystidium spp. and the rosette agent) or of mammals and birds (Rhinosporidium seeberi), and most produce uniflagellated zoospores. Fish pathogens also are found in the order Ichthyophonida, but so are saprotrophic microbes. The Ichthyophonida species do not produce flagellated cells, but many produce amoeba-like cells. This review provides descriptions of the genera that comprise the class Mesomycetozoea and highlights their morphological features, pathogenic roles, and phylogenetic relationships.
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Metabolic Diversity in Aromatic Compound Utilization by Anaerobic Microbes
Vol. 56 (2002), pp. 345–369More Less▪ AbstractA vast array of structurally diverse aromatic compounds is continually released into the environment due to the decomposition of green plants and as a consequence of human industrial activities. Increasing numbers of bacteria that utilize aromatic compounds in the absence of oxygen have been brought into pure culture in recent years. These include most major metabolic types of anaerobic heterotrophs and acetogenic bacteria. Diverse microbes utilize aromatic compounds for diverse purposes. Chlorinated aromatic compounds can serve as electron acceptors in dehalorespiration. Humic substances serve as electron shuttles to enable the use of inorganic electron acceptors, such as insoluble iron oxides, that are not always easily reduced by microbes. Substituents that are attached to aromatic rings may serve as carbon or energy sources for microbes. Examples include acyl side chains and methyl groups. Finally, aromatic compounds can be completely degraded to serve as carbon and energy sources. Routes by which various types of aromatic compounds, including toluene, ethylbenzene, phenol, benzoate, and dihydroxylated compounds, are degraded have been elucidated in recent years. Biochemical strategies employed by microbes to destabilize the aromatic ring in preparation for degradation have become apparent from this work.
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The Molecular Biology of West Nile Virus: A New Invader of the Western Hemisphere
Vol. 56 (2002), pp. 371–402More Less▪ AbstractWest Nile virus (WNV) is a mosquito-borne flavivirus that primarily infects birds but occasionally also infects humans and horses. In recent years, the frequency of WNV outbreaks in humans has increased, and these outbreaks have been associated with a higher incidence of severe disease. In 1999, the geographical distribution of WNV expanded to the Western hemisphere. WNV has a positive strand RNA genome of about 11 kb that encodes a single polyprotein. WNV replicates in the cytoplasm of infected cells. Although there are still many questions to be answered, a large body of data on the molecular biology of WNV and other flaviviruses has already been obtained. Aspects of virion structure, the viral replication cycle, viral protein function, genome structure, conserved viral elements, host factors, virus-host interactions, and vaccines are discussed in this review.
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Microbial Degradation of Polyhydroxyalkanoates*
Vol. 56 (2002), pp. 403–432More Less▪ AbstractPolyesters such as poly(3-hydroxybutyrate) (PHB) or other polyhydroxyalkanoates (PHA) have attracted commercial and academic interest as new biodegradable materials. The ability to degrade PHA is widely distributed among bacteria and fungi and depends on the secretion of specific extracellular PHA depolymerases (e-PHA depolymerases), which are carboxyesterases (EC 3.1.1.75 and EC 3.1.1.76), and on the physical state of the polymer (amorphous or crystalline). This contribution provides a summary of the biochemical and molecular biological characteristics of e-PHA depolymerases and focuses on the intracellular mobilization of storage PHA by intracellular PHA depolymerases (i-PHA depolymerases) of PHA-accumulating bacteria. The importance of different assay systems for PHA depolymerase activity is also discussed.
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Menacing Mold: The Molecular Biology of Aspergillus fumigatus
Vol. 56 (2002), pp. 433–455More Less▪ AbstractInfections with mold pathogens have emerged as an increasing risk faced by patients under sustained immunosuppression. Species of the Aspergillus family account for most of these infections, and in particular Aspergillus fumigatus may be regarded as the most important airborne pathogenic fungus. The improvement in transplant medicine and the therapy of hematological malignancies is often complicated by the threat of invasive aspergillosis. Specific diagnostic methods are still limited as are the possibilities of therapeutic intervention, leading to the disappointing fact that invasive aspergillosis is still associated with a high mortality rate that ranges from 30% to 90%. In recent years considerable progress has been made in understanding the genetics of A. fumigatus, and molecular techniques for the manipulation of the fungus have been developed. Molecular genetics offers not only approaches for the detailed characterization of gene products that appear to be key components of the infection process but also selection strategies that combine classical genetics and molecular biology to identify virulence determinants of A. fumigatus. Moreover, these methods have a major impact on the development of novel strategies leading to the identification of antimycotic drugs. This review summarizes the current knowledge on the biology, molecular genetics, and genomics of A. fumigatus.
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What are Bacterial Species?
Vol. 56 (2002), pp. 457–487More Less▪ AbstractBacterial systematics has not yet reached a consensus for defining the fundamental unit of biological diversity, the species. The past half-century of bacterial systematics has been characterized by improvements in methods for demarcating species as phenotypic and genetic clusters, but species demarcation has not been guided by a theory-based concept of species. Eukaryote systematists have developed a universal concept of species: A species is a group of organisms whose divergence is capped by a force of cohesion; divergence between different species is irreversible; and different species are ecologically distinct. In the case of bacteria, these universal properties are held not by the named species of systematics but by ecotypes. These are populations of organisms occupying the same ecological niche, whose divergence is purged recurrently by natural selection. These ecotypes can be discovered by several universal sequence-based approaches. These molecular methods suggest that a typical named species contains many ecotypes, each with the universal attributes of species. A named bacterial species is thus more like a genus than a species.
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Previous Volumes
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Volume 78 (2024)
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Volume 77 (2023)
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Volume 76 (2022)
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Volume 75 (2021)
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Volume 74 (2020)
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Volume 73 (2019)
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Volume 72 (2018)
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Volume 71 (2017)
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Volume 70 (2016)
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Volume 69 (2015)
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Volume 68 (2014)
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Volume 67 (2013)
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Volume 66 (2012)
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Volume 65 (2011)
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Volume 64 (2010)
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Volume 63 (2009)
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Volume 62 (2008)
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Volume 61 (2007)
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Volume 60 (2006)
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Volume 59 (2005)
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Volume 58 (2004)
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Volume 57 (2003)
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Volume 56 (2002)
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Volume 55 (2001)
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Volume 54 (2000)
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Volume 53 (1999)
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Volume 52 (1998)
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Volume 51 (1997)
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Volume 50 (1996)
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Volume 49 (1995)
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Volume 48 (1994)
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Volume 47 (1993)
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Volume 46 (1992)
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Volume 45 (1991)
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Volume 44 (1990)
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Volume 43 (1989)
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Volume 42 (1988)
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Volume 41 (1987)
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Volume 40 (1986)
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Volume 39 (1985)
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Volume 38 (1984)
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Volume 37 (1983)
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Volume 36 (1982)
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Volume 35 (1981)
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Volume 34 (1980)
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Volume 33 (1979)
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Volume 32 (1978)
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Volume 31 (1977)
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Volume 30 (1976)
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Volume 29 (1975)
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Volume 28 (1974)
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Volume 27 (1973)
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Volume 26 (1972)
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Volume 25 (1971)
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Volume 24 (1970)
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Volume 23 (1969)
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Volume 22 (1968)
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Volume 21 (1967)
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Volume 20 (1966)
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Volume 19 (1965)
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Volume 18 (1964)
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Volume 17 (1963)
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Volume 16 (1962)
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Volume 15 (1961)
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Volume 14 (1960)
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Volume 13 (1959)
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Volume 12 (1958)
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Volume 11 (1957)
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Volume 10 (1956)
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Volume 9 (1955)
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Volume 8 (1954)
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Volume 7 (1953)
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Volume 6 (1952)
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Volume 5 (1951)
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Volume 4 (1950)
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Volume 3 (1949)
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Volume 2 (1948)
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Volume 1 (1947)
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Volume 0 (1932)